Hunting a Rogue
by NN010
Summary: AU: In the aftermath of AOS S4; Daisy is sent undercover to root out corruption in the Alliance but later along the way gets caught up in a conspiracy to end all advanced life in the galaxy, gets her own ship, and becomes a Spectre (not in that order). It becomes up to Daisy to prove the worth of both the Inhumans and the Alliance on the galactic stage, oh and stop a rouge Spectre.
1. Prologue

Author's Note: This is gonna be the first chapter of a Mass Effect AU where versions of SHIELD seasons 1-4 happened but Daisy is reassigned to rooting out corruption in the Alliance under the guise of "giving Humanity the hero it needs" after Season 4. Also the ME games never gave specific dates for the events of the games; just the years so I'm gonna date them on my own. Also I don't think I did a good job of describing the Batarians so here's an image of one: . /masseffect/images/0/0e/Codex_ME_-_Batarians_%28after_BDTS% /revision/latest/scale-to-width-down/250?cb=20140820044603.

FFN/AO3 NOTE: Final scene has been extended with new dialogue not present on the original Tumblr post.

* * *

REQUIEM, SYSTEMS ALLIANCE BASE, VANCOUVER, BRITISH COLUMBIA, UNITED STATES OF NORTH AMERICA, MARCH 8, 2183: As Systems Alliance Lieutenant Commander, decorated N7, superhero, and undercover SHIELD agent Daisy Johnson, more commonly known by her codename, Quake, her Alliance nickname Shepard (which came to be after the then Serviceman 1st class showed excellent leadership skills during the Skyllian Blitz), or "Commander Quake" as some have taken to calling her after her promotion the previous year, stepped onto the SSV Normandy SR1 (a white Frigate (a starship "weight" mostly used as escort or scouting ships) with black accents and red stripes) she felt like she was part of something notable. While the Alliance Navy tended to name Frigates after major battles from throughout human history; naming the first ship designed by the Alliance in conjunction with the Turians (a militaristic species with bird like faces, humanoid bodies, and tribal tattoos (a turian without tattoos on their face is considered in their culture to be untrustworthy)) after a battle so (in)famous and notable that its first day came to called "D-Day" is rather appropriate. It was also the first of the new "Normandy Class" of Alliance vessels. The Normandy was a sign of improving relations between humans and turians and, (hopefully) by extension, the Citadel Council (a 3 person committee made up of the Asari (a race purely made up of humanoid blue skinned women with solid "crests" instead of hair with a penchant for Biotics), the Salarians (a species bearing a startling resemblance to the aliens seen in the alien invasion stories of the 20th century), and the Turians) that rules a good chunk of the galaxy). These improving relations are good considering that 30 years prior, humanity and the turians had been fighting against each other in the First Contact War. They remained distrusting for a couple decades after the war ended. But the Chitauri and Loki's attempted invasion of Earth in the Battle of New York 8 years ago and an encounter with Thor and the Destroyer a year prior forced the Alliance to attempt to improve relations with the Council and for SHIELD to figure out new ways to keep up as while Earth has heroes like the Avengers (who aren't in good shape themselves) to protect it, if another cosmic threat comes about, Humans and Inhumans alike will need all the help they can get. When Daisy arrived at her bunk on the Normandy she stared out the window, reflecting on key events in her life.

* * *

LOS ANGELES, UNITED STATES OF NORTH AMERICA, JANUARY 25, 2176: As the then 21 year old Daisy (then thinking she was 20) (going by the name "Skye" at the time) was going about her day, doing voice over for a Rising Tide video she was going to post to their extranet site, she heard the van door open and saw who she'd come to know as agents Phil Coulson and Grant Ward (the now 28 year old Johnson felt disgust when she saw Ward in her memory after what he'd done, Coulson chose to spare Ward on Maveth, she'd wished he killed him that day, it's not like Hive was in need of a body as Hive had managed to overpower Fitz). They then preceded to black bag her. The bag was taken off what Skye presumed was a half hour later. Skye found herself handcuffed in what Skye presumed was an interrogation room but the walls, ceiling, and floor had a honeycomb pattern that made Skye think otherwise. Coulson and Ward were both in the room with her. Skye decided to make herself sound important. "You guys have made a big mistake," she said to her captors with a hint of snark. Ward responded with "Really? You don't look that big." 'Well T-1000 over here either doesn't have a sense of humor or he's onto me,' Skye thought to herself. Coulson pulled out what looked like an Omni-Tool (an orange hologram-like cylinder that summoned around his left arm), "Look, we know you've been in contact with someone of our interest. A certain hero," Coulson said to Skye. He then laid out her options there and then: "The way I see it, you want to help this guy just as much as we do and I want to help you; so you can either work with us, or we'll let you go and let you go back to your fellow hackers and your gang friends you clearly want to escape."

* * *

SSV NORMANDY, ALLIANCE FRIGATE, VANCOUVER, BRITISH COLUMBIA, MARCH 8, 2183: Daisy remembered her first encounter with Coulson fondly, she was glad she'd taken his offer. As the Normandy began preparations to take off, Daisy started to recall what happened to Lincoln and how he- 'NO, don't go there' Daisy thought. She instead reflected on the Skyllian Blitz and her heroic actions during it:

* * *

ELYSIUM, VETUS SYSTEM, JULY 3, 2180: The then Serviceman 1st Class Johnson was on much needed shore leave at Elysium for her birthday (which was the previous day). She was in her hotel room, just having recovered from a massive hangover from the previous night when she heard gunfire. When she got outside she saw two Batarian pirates (the Batarians being a race with four eyes, human/asari type body structure, bunches of hairs on their face and cartilage formed lines on their faces) rounding up the people. Happening to have a Kessler pistol (a grey pistol that looked like a mix between a _Star Trek_ phaser and a regular gun; it used Mass Effect fields like any other modern weapon) on her, she fired at them. She managed to cap one but the other got away. She picked up the M7 Avenger assault rifle beside his body and chased after him. After a few minutes she caught up, and fired a controlled burst (so the rifle would hit its target). It did and she saved the colonists he rounded up. Daisy decided to give them a rousing speech; "Look, I know things aren't looking bright and that people you love may have died. But that doesn't mean we can't fight back and stop this attack!"

* * *

SSV NORMANDY, ALLIANCE FRIGATE, VANCOUVER, BC, MARCH 8, 2183: Daisy was taken out of her memory as she heard the PA announcement that the Normandy was about to take off. She looked out the window as the ship took off, on its way to the Charon Relay (this being one of many Mass Relays; tuning fork shaped (except for the sphere in the middle that makes the relays possible) mass transit devices used for travel between systems (as not even FTL Travel alone was fast enough for that); it's believed that an ancient, extinct race called the Protheans built the relays, scattered their beacons across the galaxy, and left knowledge of their tech for future species to find, as humans did on Mars). She looked out the window at Earth, in all its beauty.

* * *

"What about Shepard," Ambassador Donnel Udina, (a white, aging man with graying hair, and brown eyes) suggested in an audio call with two others.

"No! He's too much a loose canon! They don't call him 'the Butcher of Torfan' for nothing," Captain David Anderson (a middle aged black man with black hair and brown eyes) responded.

"Well, What about Johnson? Not much is known of her childhood," Udina then suggested, his number one candidate having been shot down, he went for who he knew was Anderson's.

"You beat me to it. She grew up an orphan, went from home to home until she was coerced into a gang at age 13 and got out and joined the Rising Tide 3 years later," Anderson explained.

"She's the only reason why Elysium is still standing," Admiral Steven Hackett (an aging white man with grey hair and blue eyes) added.

"The Alliance needs Attilan to be in our corner with the amount of Inhumans on Alliance worlds, and Johnson is best one we have in our armed forces."

"I'll make the call," Udina said before cutting the chat before calling Nihlus, a Spectre that owed Udina a favor (Spectres being agents of the Citadel Office of Special Tactics and Reconnaissance who are considered to be above galactic law).

"Nihlus, I think I have that candidate to become the first huma- I mean Inhuman, Spectre," Udina said.

"Send me the file," Nihlus simply said.

CODEX ENTRY I: Systems Alliance:

The Systems Alliance is an independent supranational government representing the collective interests of humanity as a whole. The Alliance is responsible for the governance and defense of all extra-solar colonies and stations.

The Alliance grew of the various space programs as a matter of practicality. Sol's planets had been explored and exploited through piecemeal nation efforts. The expense of colonizing entire new solar systems couldn't be met by any one country. With humans knowing that alien contact was inevitable, there was enough political will to jointly fund an international effort.

Still, the Alliance was often disregarded by those on Earth until either the First Contact War and/or the Battle of New York 17 years later (depending on who you ask). While the national governments dithered and bickered during the former over who should lead the effort to liberate Shanxi, the Alliance fleet struck decisively; and during the latter only the Alliance military could effectively aid the Avengers in quelling the invasion. Post New York public approval gave the Alliance credibility to establish its own Parliament and by then had become the galactic face of humanity.

Relations between the Inhuman city of Attilan and the Alliance have been bitter, despite the best efforts of Alliance based Inhumans like Daisy Johnson, better known to most as Quake.


	2. Chapter 1: Getting To Know The Crew

Chapter 1: Getting to Know the Crew

SSV NORMANDY, MARCH 8, 2183: Daisy felt that, as Captain Anderson's Executive Officer, she should get to know the people she was serving with as in the event Anderson was killed, stepped down, or was ashore, she would take over. She also wanted to figure out if anyone was dirty, Watchdogs or otherwise. First she went to talk to the pilot. "Hey… uh pilot guy! What's your name," Daisy asked, realizing she didn't even know the name of the Normandy's pilot. The pilot swiveled around in his chair to face her. He was wearing an SR-1 cap on his forehead, he was a white guy, face not that pale though, his iris' were a shade of green, he looked like he hadn't shaven in at least a month. "Jeff Moreau, but everyone calls me Joker." Joker introduced himself. "You must be Commander Shep- I mean Johnson. I've heard so much great things about you! My sister was on Elysium during the Skyllian Blitz! I'm so grateful you saved her life!" Joker suddenly started going from serious and angry to full fanboy in 5 seconds. "I was just doing what I felt was right, Joker," Daisy responded with. Joker's face and body language went right back to the angry and serious demeanor he'd had before. Her powers were telling her that someone was walking up behind her and she heard him say, "Hey Daisy! It's been a while! Haven't seen you since, what, like '79?" Daisy remembered who it was, "Kaiden! Yeah, it's been a while. We have a lot of catching up to do," Daisy said louder than she should have, she then realized that that last sentence had more of a sexual tone than she thought it would in her head. "That did not go how it seemed it would in my head," Daisy apologized. "It didn't sound like innuendo in my head to be honest," she added. "It's okay Commander. I don't really mind," Kaiden reassured her. Daisy breathed a sigh of relief, she'd thought it might annoy him at least, but it seems she was wrong. "I should go," Daisy said before leaving the bridge to head for the CIC. On her way out she noticed Kaiden took the co-pilot seat next to Joker. The navigator in particular caught her interest, mostly because he was behind her in the Normandy's chain of command. He seemed to notice her heading his way because he went to her. He seemed to be of mixed race descent, he had a balding head and white hair, brown eyes, and light brown facial hair and eyebrows. "Commander Johnson! Navigator Pressly. I hear we're next to each other in chain of command." Pressly introduced himself. "Well I guess it's a good idea for us to know each other for that reason," Daisy began to trail off as she noticed a turian paying close attention to her. 'That's unusual, you don't usually see turians on Alliance ships… unless he's a Spectre. But why would he be _here_ , we're just on a shakedown run to Eden Prime… Right,' Daisy asked herself. "I don't trust that guy. What business do the Turians have on an Alliance ship," Pressly asked angrily. Daisy decided to give him her theory; "My theory is that turian on deck over there (pointing at the turian walking around the CIC), is a Spectre. Of course that leaves numerous questions like 'Why would the Council get a Spectre on an Alliance ship that's on a simple shakedown run?'" "Because they want to spy on us! That's why," Pressly yelled. Kaiden then set the intercom on so he could say "Or the Council simply wants to keep an eye on their investment. This ship was a co-project with the Turians after all." Daisy then remembered that the pilot and co-pilot had access to the ships intercoms just as it's VI does. "Come on Presley! I know you're paranoid about aliens but come on! The Council isn't running some Project Insight type thing," Daisy attempted to reassure him. "Easy for you to say! You were a spy, your use to being watched," Presley yelled.

"You're just being paranoid Presley! You're not being spied on for-" Daisy started before being cut off. "Well what about the Shadow Broker? Or those terrorists calling themselves Cerberus? Hell, what about your old buddies at SHIELD? People are watching everywhere, _commander_ ," Presley ranted before heading back to his post, mentioning her rank in a condescending tone of voice. Daisy decided to head down a level… and ran into the turian. "Oh god! I am so sorry about this! I wasn't paying attention," Daisy apologized while looking up at the turian she bumped into, the one who she saw earlier in the CIC. She was able to get a good look at him. He was around 6 foot 4 (though she didn't know how Turians measured themselves), wore an armor that was black with red accents, he had reddish skin (or whatever you call skin on turians, Daisy couldn't remember at that moment), he had green eyes, and he had white tribal marks on his face. He almost reached for his gun for a second before she made the apology to him. "It's alright, you clearly weren't paying attention," the turian responded. "Nihlus Kyrik," the turian, Nihlus, introduced himself. "Daisy Johnson," Daisy introduced herself. "Well... it was nice meeting you Commander, I'll see you around," Nihlus responded with before leaving rather awkwardly. 'Weird,' Daisy thought to herself.

She walked on for a bit before seeing another man, who ran right up to her. "Commander! Commander! Corporal Richard L. Jenkins, I'm so glad to serve under you! I happen to be a fan of yours," The man, Jenkins, said enthusiastically. He looked young, though not much less than she was. She was thinking he was in his mid 20's. He had blue eyes as well. She couldn't tell what his hair color was though under his cap though. She could tell that he was very naive and full of light, ' _like I once was',_ Daisy thought to herself. 'Well, I might as well tell him what he wants to hear, he won't know I'm lying' she decided. "I'm glad to hear that. It's always nice to meet a fan", Daisy said to her fanboy turned subordinate. Jenkins turned ecstatic, "This is the best day of my life! I'm a member of the 'Quake Fan Club' extranet site!" 'Oh shit, there's even more obsessive fanboys and maybe even fangirls. Billy Koenig was right,' Daisy thought to herself.

"Commander! Joker wants you on the bridge," Kaiden said on the intercom.

"I should go," Daisy said to Jenkins.

"It's okay. You have more important things to do," Jenkins said, only a slight hint of sadness. With that Daisy went up to the bridge, having no knowledge what would happen next would be the most life-changing event in her life since she went through Terrigenesis.

CODEX ENTRY II: Terrigenesis: Terrigenesis is the process Inhumans go through to develop their latent superhuman abilities. Specialized crystals called Terrigen Crystals from the long dead alien race the Kree are used to create the mists that kick-start the process. The Inhuman Royal Family of Attilan use a caste societal system to maintain order, enslaving those who don't gain valuable enough powers. However it's known that royal family member Maximus didn't gain powers of any kind. Though Attilan is nowhere near as strict with Terrigenesis as Afterlife was. It's leader, the late Jiaying, only allowed certain people to go through the process. She is mostly remembered today as the mother of influential Inhuman Daisy Johnson.


	3. Update

Sorry this isn't a new chapter but I'm gonna start a Fallout 4 fic to get my creative juices flowing again! Hopefully soon I'll be able to work on Hunting a Rogue and Shadows from the Past again but I just need a change of pace right now and this Fallout fic will provide that. Plus it's been in the forefront of my mind for a while now! So, hope you read  
"Two Sides to a Story" (the Fallout fic) and I hope to return to Marvel fanfics soon!


End file.
